Efficient HIV-1 inhibition by a 16 nt-long RNA aptamer designed by combining in vitro selection and in silico optimisation strategies

Abstract

The human immunodeficiency virus type-1 (HIV-1) genome contains multiple, highly conserved structural RNA domains that play key roles in essential viral processes. Interference with the function of these RNA domains either by disrupting their structures or by blocking their interaction with viral or cellular factors may seriously compromise HIV-1 viability. RNA aptamers are amongst the most promising synthetic molecules able to interact with structural domains of viral genomes. However, aptamer shortening up to their minimal active domain is usually necessary for scaling up production, what requires very time-consuming, trial-and-error approaches. Here we report on the in vitro selection of 64 nt-long specific aptamers against the complete 5′-untranslated region of HIV-1 genome, which inhibit more than 75% of HIV-1 production in a human cell line. The analysis of the selected sequences and structures allowed for the identification of a highly conserved 16 nt-long stem-loop motif containing a common 8 nt-long apical loop. Based on this result, an in silico designed 16 nt-long RNA aptamer, termed RNApt16, was synthesized, with sequence 5′-CCCCGGCAAGGAGGGG-3′. The HIV-1 inhibition efficiency of such an aptamer was close to 85%, thus constituting the shortest RNA molecule so far described that efficiently interferes with HIV-1 replication.

Functional Information Stored in the Conserved Structural RNA Domains of Flavivirus Genomes

“…They also provide an interesting means of developing molecular tools for deciphering the functional role of genomic structural elements, and therefore the identification of potential therapeutic targets. This has already been shown for other, closely related viruses such as HCV (Marton et al, 2011, 2013; Fernández-Sanlés et al, 2015) as well as non-related viruses such as HIV (Sánchez-Luque et al, 2014). Aptamers can be chemically modified quite easily to increase their stability and improve their efficiency.…”

Use of Aptamers as Diagnostics Tools and Antiviral Agents for Human Viruses

“…Those aptamers inhibited more than 75% of HIV-1 production in a human cell line. The analysis of the selected sequences and structures allowed for the identification of a highly conserved 16 nt-long stem-loop motif containing a common 8 nt-long apical loop (RNApt16; 5′-CCCCGGCAAGGAGGGG-3′) that produced an HIV-1 inhibition close to 85%, thus constituting the shortest RNA molecule so far described that efficiently interferes with HIV-1 replication [29]. The reason to use RNA aptamer is to go into the cell as DNA plasmid and to get intracellular expression of RNA aptamer to block the target.…”

Oligonucleotide aptamers: promising and powerful diagnostic and therapeutic tools for infectious diseases

“…90 , 95 Besides anti-RT aptamers, highly specific aptamers-that target various parts of the HIV-1 genome, the trans-activation-responsive (TAR) RNA element, or HIV-1 integrase, nucleocapsid, Gag or Rev proteins-have been isolated and shown to effectively suppress viral replication. [96][97][98][99][100][101][102][103][104][105][106] HCV HCV is the common cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. 107 There is currently no approved HCV vaccine, and aptamer research for the diagnosis and treatment in this area is at the initial stages.…”